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- PDB-9cwl: Crystal structure of outer membrane lipoprotein carrier protein (... -

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Basic information

Entry
Database: PDB / ID: 9cwl
TitleCrystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (monoclinic P Form)
ComponentsOuter membrane lipocarrier LolA family protein
KeywordsLIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / lipoprotein carrier / LolA
Function / homologyOuter membrane lipoprotein carrier protein LolA-like / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / protein transport / metal ion binding / Outer membrane lipocarrier LolA family protein
Function and homology information
Biological speciesFrancisella philomiragia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (monoclinic P Form)
Authors: Lovell, S. / Taylor, K.E. / Cooper, A. / Battaile, K.P. / Buchko, G.W.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane lipocarrier LolA family protein


Theoretical massNumber of molelcules
Total (without water)22,1951
Polymers22,1951
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.103, 64.118, 35.471
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer membrane lipocarrier LolA family protein


Mass: 22194.951 Da / Num. of mol.: 1 / Fragment: L32-N205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella philomiragia (bacteria) / Gene: Fphi_1079 / Plasmid: FrphA.20731.a.VL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0TX44
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2. FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well A9 drop2, Puck: ...Details: Morpheus A9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2. FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well A9 drop2, Puck: PSL0911 and PSL0912 merged, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 27, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→33.96 Å / Num. obs: 14044 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.065 / Rrim(I) all: 0.165 / Χ2: 1.03 / Net I/σ(I): 9.8 / Num. measured all: 92640
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.696 / Num. measured all: 5816 / Num. unique obs: 855 / CC1/2: 0.719 / Rpim(I) all: 0.707 / Rrim(I) all: 1.839 / Χ2: 0.92 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(dev_5396: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.96 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 643 4.61 %
Rwork0.1888 --
obs0.1905 13961 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 0 102 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111237
X-RAY DIFFRACTIONf_angle_d1.0821683
X-RAY DIFFRACTIONf_dihedral_angle_d17.225458
X-RAY DIFFRACTIONf_chiral_restr0.065206
X-RAY DIFFRACTIONf_plane_restr0.008213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.25331460.24362649X-RAY DIFFRACTION99
1.94-2.130.28651300.19742644X-RAY DIFFRACTION100
2.13-2.440.23931080.19262655X-RAY DIFFRACTION99
2.44-3.080.2303990.20972685X-RAY DIFFRACTION100
3.08-33.960.19981600.16732685X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.06854.55973.65935.61582.8444.147-0.15810.1389-0.05810.11020.10320.0027-0.23060.10260.03230.1403-0.0052-0.01020.10080.01440.11370.3624-5.20397.1739
24.6024-0.6524-1.0885.46141.94274.1961-0.05010.29270.0156-0.4103-0.013-0.3159-0.35440.13190.10780.2072-0.0357-0.0110.26470.02630.239112.7527-8.94763.1245
32.57790.39940.60272.889-0.78224.65910.01490.07160.05510.03560.0097-0.0829-0.0697-0.0148-0.02080.14420.02160.01340.1085-0.00710.15332.98136.4799-0.2422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 205 )

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